Bivalent bromodomain inhibitors and uses thereof

Abstract

The present invention provides bivalent inhibitors of BET bromodomains, such as compounds of Formulae (I), (II), (III), (IV), (V), and (VI). Some bromodomain-containing proteins (e.g., BRD4) have a tandem bromodomain primary structure comprising more than one bromodomain binding site (e.g., BRD4 comprises BD1 and BD2). Bivalent inhibitors of BET bromodomains provided herein can target bromodomains through advantageous multivalent interactions, and can therefore can be to treat diseases or conditions associated with bromodomain-containing proteins. The present also provides pharmaceutical compositions and kits comprising the inventive compounds, as well as methods of using the inventive compounds.

1 . A compound of Formula (I): 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, wherein:
 L is a linker comprising 1-40 carbon atoms, selected from the group consisting of optionally substituted alkylene, optionally substituted heteroalkylene, optionally substituted alkenylene, optionally substituted heteroalkenylene, optionally substituted alkynylene, optionally substituted heteroalkynylene, optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, optionally substituted heteroarylene, and any combination thereof; 
 each instance of R 1 , R 2 , R 3 , and R 4  is independently hydrogen, halogen, —CN, —NO 2 , —N 3 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, —OR a , —N(R b ) 2 , or —SR c ; 
 each instance of R a  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or an oxygen protecting group; 
 each instance of R b  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group; or optionally two R b  are joined together with the intervening carbon atoms to form optionally substituted heterocyclyl or optionally substituted heteroaryl; 
 each instance of R c  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a sulfur protecting group; 
 R 5  is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted aralkyl, optionally substituted heteroarylalkyl, optionally substituted heterocyclylalkyl, optionally substituted carbocyclylalkyl, optionally substituted acyl, —OR 5a , or —N(R 5b ) 2 ; 
 each instance of R 5a  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted aralkyl, optionally substituted heteroarylalkyl, optionally substituted heterocyclylalkyl, optionally substituted carbocyclylalkyl, optionally substituted acyl, or an oxygen protecting group; 
 each instance of R 5b  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted aralkyl, optionally substituted heteroarylalkyl, optionally substituted heterocyclylalkyl, optionally substituted carbocyclylalkyl, optionally substituted acyl, or a nitrogen protecting group; or optionally two R 5b  are joined together with the intervening carbon atoms to form optionally substituted heterocyclyl or optionally substituted heteroaryl; and 
 each instance of m is independently 0, 1, 2, 3, 4, or 5. 
 
     
     
         2 - 13 . (canceled) 
     
     
         14 . A compound of Formula (III): 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, wherein:
 L is a linker comprising 1-40 carbon atoms, selected from the group consisting of optionally substituted alkylene, optionally substituted heteroalkylene, optionally substituted alkenylene, optionally substituted heteroalkenylene, optionally substituted alkynylene, optionally substituted heteroalkynylene, optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, optionally substituted heteroarylene, and any combination thereof; 
 each instance of R 1 , R 2 , R 3 , and R 4  is independently each instance of R 4  is independently hydrogen, halogen, —CN, —NO 2 , —N 3 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, —OR a , —N(R b ) 2 , or —SR c ; 
 each instance of R a  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or an oxygen protecting group; 
 each instance of R b  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group; or optionally two R b  are joined together with the intervening carbon atoms to form optionally substituted heterocyclyl or optionally substituted heteroaryl; 
 each instance of R c  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a sulfur protecting group; 
 each instance of R 5  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted aralkyl, optionally substituted heteroarylalkyl, optionally substituted heterocyclylalkyl, optionally substituted carbocyclylalkyl, optionally substituted acyl, —OR 5a , or —N(R 5b ) 2 ; 
 each instance of R 5a  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted aralkyl, optionally substituted heteroarylalkyl, optionally substituted heterocyclylalkyl, optionally substituted carbocyclylalkyl, optionally substituted acyl, or an oxygen protecting group; 
 each instance of R 5b  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted aralkyl, optionally substituted heteroarylalkyl, optionally substituted heterocyclylalkyl, optionally substituted carbocyclylalkyl, optionally substituted acyl, or a nitrogen protecting group; or optionally two R 5b  are joined together with the intervening carbon atoms to form optionally substituted heterocyclyl or optionally substituted heteroaryl; and 
 each instance of m is independently 0, 1, 2, 3, 4, or 5. 
 
     
     
         15 - 17 . (canceled) 
     
     
         18 . A compound of Formula (IV): 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, wherein:
 L is a linker comprising 1-40 carbon atoms, selected from the group consisting of optionally substituted alkylene, optionally substituted heteroalkylene, optionally substituted alkenylene, optionally substituted heteroalkenylene, optionally substituted alkynylene, optionally substituted heteroalkynylene, optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, optionally substituted heteroarylene, and any combination thereof; 
 each instance of R 1 , R 2 , R 3 , and R 4  is independently hydrogen, halogen, —CN, —NO 2 , —N 3 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, —OR a , —N(R b ) 2 , or —SR c ; 
 each instance of R a  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or an oxygen protecting group; 
 each instance of R b  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group; or optionally two R b  are joined together with the intervening carbon atoms to form optionally substituted heterocyclyl or optionally substituted heteroaryl; 
 each instance of R c  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a sulfur protecting group; 
 each instance of m is independently 0, 1, 2, 3, 4, or 5; 
 each instance of R 6 , R 7 , R 10 , and R 11  is independently hydrogen, halogen, —CN, —NO 2 , —N 3 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, —OR a , —N(R b ) 2 , or —SR c ; 
 R 9  is hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, —OR a , —N(R b ) 2 , or —SR c ; 
 R 8  is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or an oxygen protecting group; 
 p is 0, 1, 2, or 3; and 
 q is 0, 1, 2, 3, or 4. 
 
     
     
         19 - 21 . (canceled) 
     
     
         22 . A compound of Formula (V): 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, wherein:
 L is a linker comprising 1-40 carbon atoms, selected from the group consisting of optionally substituted alkylene, optionally substituted heteroalkylene, optionally substituted alkenylene, optionally substituted heteroalkenylene, optionally substituted alkynylene, optionally substituted heteroalkynylene, optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, optionally substituted heteroarylene, and any combination thereof; 
 each instance of R 1 , R 3 , and R 4  is independently hydrogen, halogen, —CN, —NO 2 , —N 3 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, —OR a , —N(R b ) 2 , or —SR c ; 
 each instance of R a  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or an oxygen protecting group; 
 each instance of R b  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group; or optionally two R b  are joined together with the intervening carbon atoms to form optionally substituted heterocyclyl or optionally substituted heteroaryl; 
 each instance of R c  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a sulfur protecting group; 
 R 5  is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted aralkyl, optionally substituted heteroarylalkyl, optionally substituted heterocyclylalkyl, optionally substituted carbocyclylalkyl, optionally substituted acyl, —OR 5a , or —N(R 5b ) 2 ; 
 each instance of R 5a  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted aralkyl, optionally substituted heteroarylalkyl, optionally substituted heterocyclylalkyl, optionally substituted carbocyclylalkyl, optionally substituted acyl, or an oxygen protecting group; 
 each instance of R 5b  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted aralkyl, optionally substituted heteroarylalkyl, optionally substituted heterocyclylalkyl, optionally substituted carbocyclylalkyl, optionally substituted acyl, or a nitrogen protecting group; or optionally two R 5b  are joined together with the intervening carbon atoms to form optionally substituted heterocyclyl or optionally substituted heteroaryl; 
 each instance of m is independently 0, 1, 2, 3, 4, or 5; 
 each instance of R 6 , R 7 , R 10 , and R 11  is independently hydrogen, halogen, —CN, —NO 2 , —N 3 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, —OR a , —N(R b ) 2 , or —SR c ; 
 R 9  is hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, —OR a , —N(R b ) 2 , or —SR c ; 
 R 8  is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or an oxygen protecting group; 
 p is 0, 1, 2, or 3; and 
 q is 0, 1, 2, 3, or 4. 
 
     
     
         23 - 26 . (canceled) 
     
     
         27 . A compound of Formula (VI): 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, wherein:
 L is a linker comprising 1-40 carbon atoms, selected from the group consisting of optionally substituted alkylene, optionally substituted heteroalkylene, optionally substituted alkenylene, optionally substituted heteroalkenylene, optionally substituted alkynylene, optionally substituted heteroalkynylene, optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, optionally substituted heteroarylene, and any combination thereof; 
 each instance of R 6 , R 7 , R 10 , and R 11  is independently hydrogen, halogen, —CN, —NO 2 , —N 3 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, —OR a , —N(R b ) 2 , or —SR c ; 
 each instance of R 9  is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, —OR a , —N(R b ) 2 , or —SR c ; 
 each instance of R a  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or an oxygen protecting group; 
 each instance of R b  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group; or optionally two R b  are joined together with the intervening carbon atoms to form optionally substituted heterocyclyl or optionally substituted heteroaryl; 
 each instance of R c  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a sulfur protecting group; 
 each instance of R 8  is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or an oxygen protecting group; 
 p is 0, 1, 2, or 3; and 
 q is 0, 1, 2, 3, or 4. 
 
     
     
         28 - 92 . (canceled) 
     
     
         93 . The compound of  claim 1 , wherein the compound is selected from the group consisting of: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
       and pharmaceutically acceptable salts and tautomers thereof. 
     
     
         94 - 96 . (canceled) 
     
     
         97 . The compound of  claim 14 , wherein the compound is selected from the group consisting of: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
       and pharmaceutically acceptable salts and tautomers thereof. 
     
     
         98 . (canceled) 
     
     
         99 . The compound of  claim 18 , wherein the compound is selected from the group consisting of: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
       and pharmaceutically acceptable salts and tautomers thereof. 
     
     
         100 . (canceled) 
     
     
         101 . The compound of  claim 22 , wherein the compound is selected from the group consisting of: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
       and pharmaceutically acceptable salts and tautomers thereof. 
     
     
         102 . (canceled) 
     
     
         103 . The compound of  claim 27 , wherein the compound is selected from the group consisting of: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
       and pharmaceutically acceptable salts and tautomers thereof. 
     
     
         104 . A pharmaceutical composition comprising a compound of  claim 1 , or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, and a pharmaceutically acceptable excipient. 
     
     
         105 . A kit comprising a container, a compound of  claim 1 , or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, or a pharmaceutical composition thereof, and instructions for administering the compound or composition to a subject. 
     
     
         106 . A method of treating a disease associated with a bromodomain or a bromodomain-containing protein in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of a compound of  claim 1 , or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, or a pharmaceutical composition thereof. 
     
     
         107 . (canceled) 
     
     
         108 . A method of treating a disease associated with aberrant activity of a bromodomain or a bromodomain-containing protein in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of a compound of  claim 1 , or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, or a pharmaceutical composition thereof. 
     
     
         109 - 110 . (canceled) 
     
     
         111 . A method for male contraception, the method comprising administering to a male subject in need thereof an effective amount of a compound of  claim 1 , or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, or a pharmaceutical composition thereof. 
     
     
         112 . A method of inhibiting the activity of a bromodomain or a bromodomain-containing protein in a subject or a biological sample, the method comprising administering to the subject or contacting the biological sample with an effective amount of a compound of  claim 1 , or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, or a pharmaceutical composition thereof. 
     
     
         113 - 115 . (canceled) 
     
     
         116 . A method of inhibiting the binding of a bromodomain-containing protein to an acetyl-lysine residue of a second protein in a subject or a biological sample, the method comprising administering to the subject or contacting the biological sample with an effective amount of a compound of  claim 1 , or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, or a pharmaceutical composition thereof, wherein the second protein is a protein with an acetyl-lysine residue. 
     
     
         117 - 118 . (canceled) 
     
     
         119 . A method of inhibiting the expression of a gene that is regulated by a bromodomain-containing protein in a subject or a biological sample, the method comprising administering to the subject or contacting the biological sample with an effective amount of a compound of  claim 1 , or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, or a pharmaceutical composition thereof. 
     
     
         120 . (canceled) 
     
     
         121 . A method of inducing apoptosis in cell of a subject or a biological sample, the method comprising administering to the subject or contacting the biological sample with an effective amount of a compound of  claim 1 , or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, or a pharmaceutical composition thereof. 
     
     
         122 . (canceled) 
     
     
         123 . A method of inducing G1 arrest in a cell of a subject or a biological sample, the method comprising administering to the subject or contacting the biological sample with an effective amount of a compound of  claim 1 , or a pharmaceutically acceptable salt, stereoisomer, or tautomer thereof, or a pharmaceutical composition thereof. 
     
     
         124 - 152 . (canceled)